May 20, 2020

Greetings from Pittsburgh, PA!

Television and movies are a welcome distraction from the current global pandemic. For this digest, I’d like to highlight two articles. The article by Sajjad et al. investigates the possibility of resurrection of ancient microbes present in the natural frozen world and is a perfect pair for the monster-of-the-week X-Files episode “Ice.” The second highlighted article focuses on the microbiome present on two ancient Slavonic parchment codices and how this data can be used to provide additional historical context. Maybe Harrison Ford can team up with Piñar et al. to create a fourth movie in the Indiana Jones Franchise based on their work?

Happy reading, everyone!

General microbiome

Effect of a novel synbiotic on Streptococcus mutans – Bijle et al. – Nature Scientific Reports

Culturomics‐based genomics sheds light on the ecology of the new haloarchaeal genus Halosegnis – Durán‐Viseras et al. – Environmental Microbiology

Review: Ecological features of the persistence of Vibrio cholerae: retrospective analysis and actual state of the problem – Menshikova et al. – Jounral of microbiology, epidemiology, and immunobiology

Metagenome-assembled genomes reveal unique metabolic adaptations of a basal marine Thaumarchaeota lineage – Reji and Francis – ISME Journal

Homoplastic single nucleotide polymorphisms contributed to phenotypic diversity in Mycobacterium tuberculosis – Tantivitayakul et al. – Nature Scientific Reports

Plant, root, and soil microbiome

Impacts of forest conversion to plantations on the soil carbon and nitrogen dynamics, and microbial communities – Wang et al. – Soil Biology and Biochemistry

Water and extremophile microbiome

Novel yeast taxa from the cold: description of Cryolevonia giraudoae sp. nov. and Camptobasidium gelus sp. nov. – de Garcia et al. – International Journal of Systematic and Evolutionary Microbiology

Remote sensing reveals Antarctic green snow algae as important terrestrial carbon sink – Gray et al. – Nature Communications

Review: Resurrection of inactive microbes and resistome present in the natural frozen world: Reality or myth? – Sajjad et al. – Science of the Total Environment

Built environment

Decoding the biological information contained in two ancient Slavonic parchment codices: an added historical value – Piñar et al. – Environmental Microbiology

Bioinformatics

Preprint: Efficiently processing amplicon sequencing data for microbial ecology with dadasnake, a DADA2 implementation in Snakemake – Weißbecker et al. – bioRxiv

Techniques

Editorial: Visualizing the invisible: class excursions to ignite children’s enthusiasm for microbes – McGenity et al. – Microbial Biotechnology

Discovery of thermophilic Bacillales using reduced-representation genotyping for identification – Talamantes-Becerra et al. – BMC Microbiology

May 6, 2020

General microbiome

Multi-proxy analyses of a mid-15th century Middle Iron Age Bantu-speaker palaeo-faecal specimen elucidates the configuration of the ‘ancestral’ sub-Saharan African intestinal microbiome – Rifkin et al – Microbiome

The neovaginal microbiome of transgender women post-gender reassignment surgery  – Birse et al – Microbiome

Pregnancy and early life

The stepwise assembly of the neonatal virome is modulated by breastfeeding – Liang et al – Nature

Human gut microbiome

Impact of smoking cessation, coffee and bread consumption on the intestinal microbial composition among Saudis: A cross-sectional study – Harakeh et al – PLOS One

Animal experiments

Altered Immunity of Laboratory Mice in the Natural Environment Is Associated with Fungal Colonization – Yeung et al – Cell Host & Microbe

Infection with the sheep gastrointestinal nematode Teladorsagia circumcincta increases luminal pathobionts – Cortés et al – Microbiome

Vitamin D receptor promotes healthy microbial metabolites and microbiome – Chatterjee et al – Nature Scientific Reports

Phages and viruses

Phages Actively Challenge Niche Communities in Antarctic Soils – Bezuidt et al – mSystems

Evolution

The Syntrophy hypothesis for the origin of eukaryotes revisited – López-García & Moreira – Nature Microbiology

Microbes in the news

State-of-the-art imaging method provides new insights into how bacteria move and exchange genetic information

April 11, 2020

Happy Saturday morning, y’all! I’m excited for my first contribution to the digest, and hope you enjoy my picks over a luxurious weekend meal. Today’s digest starts with some preprints about COVID including research on a drug that may inhibit viral replication. Other research highlights include an examination of the relationship between the vaginal microbiome and pre-term birth, a preprint on the oral microbiome in space, and a potential new technique for low cost, high-throughput metagenome profiling. Scroll all the way to the end for information about a fun project by a University of Wyoming student called The Microbestiary.

COVID-19
Preprint: Genomic determinants of pathogenicity in SARS-CoV-2 and other human coronaviruses. Auslander, N. et al.

Preprint: Nelfinavir inhibits replication of severe acute respiratory syndrome coronavirus 2 in vitro. Yamamoto, N. et al.

Preprint: Understanding the B and T cells epitopes of spike protein of severe respiratory syndrome coronavirus-2: A computational way to predict the immunogens. Vashi, Y. et al.

General Microbiome
Preprint: From iron to antibiotics: Identification of conserved bacterial-fungal interactions across diverse partners. Pierce, EC. et al.

Human Gut Microbiome
Review: Unraveling Host-Gut Microbiota Dialogue and Its Impact on Cholesterol Levels. Villette R. et al. Frontiers in Pharmacology.

Metagenomics analysis reveals features unique to Indian distal gut microbiota. Kaur, K. et al. PLOS ONE.

Gut Microbiota Modulate CD8 T Cell Responses to Influence Colitis-Associated Tumorigenesis. Yu, A.I. et al. Cell Reports.

Human Oral Microbiome
Preprint: Characterization of the oral microbiome of medically controlled type-2 diabetes patients. Santos, A. et al.

Human Vaginal Microbiome
Cervicovaginal microbiome and natural history of HPV in a longitudinal study. Usyk, M. et al. PLOS Pathogens.

Meta-Analysis of Vaginal Microbiome Data Provides New Insights Into Preterm Birth. Kosti, I. et al. Frontiers in Microbiology.

Water and Extremophile Microbiome
Microbiota characterization of Exaiptasia diaphana from the Great Barrier Reef. Hartman, L.M. et al. Animal Microbiome.

Microbial Diversity and Metabolic Potential in the Stratified Sansha Yongle Blue Hole in the South China Sea. He, P. et al. Scientific Reports.

Metabolic versatility of freshwater sedimentary archaea feeding on different organic carbon sources. Compte-Port, S. et al. PLOS ONE.

Animal Experiments and Animal Microbiome
The skin microbiome facilitates adaptive tetrodotoxin production in poisonous newts. Vaelli, P.M. et al. eLife.

Metatranscriptomic virome assessment of Rhipicephalus microplus from Colombia. Gomez, G.F. et al. Ticks and Tick-borne Diseases.

Preprint: Metabolic differences between symbiont subpopulations in the deep-sea tubeworm Riftia pachyptila. Hinzke, T. et al.

Preprint: Similar gut bacterial microbiota in two fruit-feeding moth pests collected from different host species and locations. Gong, Q et al.

Plant, Root, and Soil Microbiome
The preceding root system drives the composition and function of the rhizosphere microbiome. Zhou, Y. et al. Genome Biology.

Microbial Co-Occurrence in Floral Nectar Affects Metabolites and Attractiveness to a Generalist Pollinator. Rering, C.C. et al. Journal of Chemical Ecology.

Impact of phages on soil bacterial communities and nitrogen availability under different assembly scenarios. Braga, L.P.P. et al. Microbiome.

A predatory myxobacterium controls cucumber Fusarium wilt by regulating the soil microbial community. Ye, X. et al. Microbiome.

A plant genetic network for preventing dysbiosis in the phyllosphere. Chen, T. et al. Nature.

Fungal communities differentially respond to warming and drought in tropical grassland soil. de Oliveira, T.B. et al. Molecular Ecology.

Built Environment
An in-depth survey of the microbial landscape of the walls of a neonatal operating room. Derilus, D. et al. PLOS ONE.

Microbes in Space
Preprint: Defining the resilience of the human salivary microbiota by a 520 days longitudinal study in confined environment: the Mars500 mission. Bacci, G. et al.

Phages and Viruses
Phage cocktail containing Podoviridae and Myoviridae bacteriophages inhibits the growth of Pectobacterium spp. under in vitro and in vivo conditions. Zaczek-Moczydłowska, M.A. et al. PLOS ONE.

Dynamic genome evolution and complex virocell metabolism of globally-distributed giant viruses. Moniruzzaman M., et al. Nature Communications.

Preprint: Infection with novel Bacteroides phage BV01 alters host transcriptome and bile acid metabolism in a common human gut microbe. Campbell, D.E. et al.

Bioinformatics
Preprint: Integrative and Conjugative Elements (ICE) and Associated Cargo Genes within and across Hundreds of Bacterial Genera. Kaufman, J. et al.

Techniques
A restriction enzyme reduced representation sequencing approach for low-cost, high-throughput metagenome profiling. Hess, M.K. et al. PLOS ONE.

Industrial Microbiome
Open microbiome dominated by Clostridium and Eubacterium converts methanol into i-butyrate and n-butyrate. Huang, S. et al. Applied Microbiology and Biotechnology.

Fun with Microbes
University of Wyoming masters student Erin Bentley was selected for an Arctic Circle Expedition in 2021 where she will characterize microbes and share her discoveries on The Microbestiary.
“The Microbestiary strives to show the public, in welcoming and memorable ways, that the microbial world is populated by strange and beautiful characters,” says Bentley in an article published on the UW website.

September 17, 2019

Happy Tuesday! Today’s digest includes wastewater treatment biofilms, the microbiome during Crohn’s disease remission, and the bacteria associated with acid mine drainage. Enjoy!

Human oral microbiome

Succession of oral microbiota community as a tool to estimate postmortem interval – Dong – Scientific Reports

Human gut microbiome

Remission in Crohn’s disease is accompanied by alterations in the gut microbiota and mucins production – Magro – Scientific Reports

Specific gut microbiome members are associated with distinct immune markers in pediatric allogeneic hematopoietic stem cell transplantation – Ingham – Microbiome

Effect of a Chinese medical nutrition therapy diet on gut microbiota and short chain fatty acids in the simulator of the human intestinal microbial ecosystem (SHIME) – Wu – Journal of Functional Foods

A comprehensive assessment of demographic, environmental, and host genetic associations with gut microbiome diversity in healthy individuals – Scepanovic – Microbiome

Animal experiments

Dietary Bovine Milk Exosomes Elicit Changes in Bacterial Communities in C57BL/6 Mice – Zhou – American Journal of Physiology

Microbial Metabolism Modulates Antibiotic Susceptibility within the Murine Gut Microbiome – Cabral – Cell Metabolism

Animal microbiome

Maternal vs artificial rearing shapes the rumen microbiome having minor long‐term physiological implications – Belanche – Environmental Microbiology

Plant, root, and soil microbiome

Impact of continuous Panax notoginseng plantation on soil microbial and biochemical properties – Zhang – Scientific Reports

Three Bermudagrass-suppression techniques have little effect on soil-nutrient availability and microbial communities 200 days after application – Farthing – Applied Soil Ecology

Water and extremophile microbiome

Effect of salinity on mature wastewater treatment biofilm microbial community assembly and metabolite characteristics – Wang – Science of the Total Environment

Diversity and functional profile of bacterial communities at Lancaster acid mine drainage dam, South Africa as revealed by 16S rRNA gene high-throughput sequencing analysis – Lukhele – Extremophiles

Abiotic stress resistance, plant growth promotion and antifungal potential of halotolerant bacteria from a Tunisian solar saltern – Masmoudi – Microbiological Research

Built environment

Effective removal of antibiotic resistance genes and potential links with archaeal communities during vacuum-type composting and positive-pressure composting – Fan – Journal of Environmental Science

Hydraulically Fractured Natural-Gas Well Microbial Communities Contain Genomic Halogenation and Dehalogenation Potential – Evans – Environmental Science & Technology Letters

Successional trophic complexity and biogeographical structure of eukaryotic communities in waterworks rapid sand filters – Harder – FEMS Microbiology Ecology

May 16, 2019

Today’s digest includes the microbial communities of fruit peels, bacterial crude oil degradation, and the gut microbiome of sea cucumbers. Enjoy!

Pregnancy and early life

Preprint: Interactions between the gut microbiome and mucosal immunoglobulins A, M and G in the developing infant gut – Janzon – BioRxiv

Human gut microbiome

Evolution of the gut microbiome following acute HIV-1 infection – Rocafort – Microbiome

Animal microbiome

Evaluation of the Function of Wild Animal Gut Microbiomes Using Next-Generation Sequencing and Bioinformatics and its Relevance to Animal Conservation – Yao – Evolutionary Bioinformatics

High-throughput sequencing of 16S rRNA amplicons characterizes gut microbiota shift of juvenile sea cucumber Apostichopus japonicus feeding with three antibiotics – Zhao – Journal of Oceanology and Limnology

Plant, root, and soil microbiome

Contrasting patterns and drivers of soil fungal communities in subtropical deciduous and evergreen broadleaved forests – Chen – Applied Microbiology and Biotechnology

Evaluation of microbial communities in peels of Brazilian tropical fruits by amplicon sequence analysis – Cruz – Brazilian Journal of Microbiology

Assembly mechanisms of soil bacterial communities in subalpine coniferous forests on the Loess Plateau, China – Zhao – Journal of Microbiology

Evaluating the effects of canine urine on urban soil microbial communities – Lee – Urban Ecosystems

Methane emission and soil microbial communities in early rice paddy as influenced by urea-N fertilization – Liu – Plant and Soil

Rhizosphere carbon supply accelerates soil organic matter decomposition in the presence of fresh organic substrates – Jackson – Plant and Soil

The relative contributions of pH, organic anions, and phosphatase to rhizosphere soil phosphorus mobilization and crop phosphorus uptake in maize/alfalfa polyculture – Sun – Plant and Soil

Diversity of anammox bacteria and abundance of functional genes for nitrogen cycling in the rhizosphere of submerged macrophytes in a freshwater lake in summer – Zhao – Journal of Soils and Sediments

Direct and indirect effects of elevated CO2 and nitrogen addition on soil microbial communities in the rhizosphere of Bothriochloa ischaemum – Xiao – Journal of Soils and Sediments

Rhizocompartments and environmental factors affect microbial composition and variation in native plants – Kang – Journal of Microbiology

The inhibitory effect of cadmium and/or mercury on soil enzyme activity, basal respiration, and microbial community structure in coal mine–affected agricultural soil – Zheng – Annals of Microbiology

Water and extremophile microbiome

Preprint: Metabolic Architecture of the Deep Ocean Microbiome – Acinas – BioRxiv

Production of Current by Syntrophy Between Exoelectrogenic and Fermentative Hyperthermophilic Microorganisms in Heterotrophic Biofilm from a Deep-Sea Hydrothermal Chimney – Pillot – Microbial Ecology

A glimpse of the prokaryotic diversity of the Large Aral Sea reveals novel extremophilic bacterial and archaeal groups – Shurigin – MicrobiologyOpen

Molecular analyses of bacterioplankton communities with highly abundant Vibrio clades: a case study in Bohai Sea coastal waters – Wang – Journal of Oceanology and Limnology

Archaeal communities in the deep-sea sediments of the South China Sea revealed by Illumina high-throughput sequencing – Li – Annals of Microbiology

Bacterial succession and co‐occurrence patterns of an enriched marine microbial community during light crude oil degradation in a batch reactor – Uribe‐Flores – Journal of Applied Microbiology

Microbial assemblages reflect environmental heterogeneity in alpine streams – Hotaling – Global Change Biology

Food microbiology

Bacterial community dynamics in lait caillé, a traditional product of spontaneous fermentation from Senegal – Groenenboom – PLoS One

March 27, 2019

Happy Wednesday! Today’s digest includes spider endosymbionts, microbes shared between family members, and the effects of plastic on the microbiome of compost. Enjoy!

General microbiome

Transmission of human-associated microbiota along family and social networks – Brito – Nature Microbiology

Diversity-disease relationships and shared species analyses for human microbiome-associated diseases – Ma – ISME

Dispersal homogenizes communities via immigration even at low rates in a simplified synthetic bacterial metacommunity – Fodelianakis – Nature Communications

Preprint: Exploring the archaeome: detection of archaeal signatures in the human body – Pausan – bioRxiv

Human gut microbiome

Sucrose 6F-phosphate phosphorylase: a novel insight in the human gut microbiome – Tauzin – Microbial Genomics

Human skin microbiome

Preprint: Moving microbes: the dynamics of transient microbial residence on human skin – Vandegrift – bioRxiv

Animal experiments

Effects of phycocyanin in modulating the intestinal microbiota of mice – Xie – MicrobiologyOpen

Animal microbiome

Preprint: Endosymbiotic bacteria are prevalent and diverse in agricultural spiders – White – bioRxiv

Plant, root, and soil microbiome

Litter Quality Modulates Effects of Dissolved Nitrogen on Leaf Decomposition by Stream Microbial Communities – Jabiol – Microbial Ecology

Additions of sugar and nitrogenous fertiliser affect plant nitrogen status and soil microbial communities – Morrow – Applied Soil Ecology

Characterizing differences in microbial community composition and function between Fusarium wilt diseased and healthy soils under watermelon cultivation – Wang – Plant and Soil

Meta-analysis shows positive effects of plant diversity on microbial biomass and respiration – Chen – Nature Communications

Effects of transgenic glufosinate-tolerant rapeseed (Brassica napus L.) and the associated herbicide application on rhizospheric bacterial communities – Tang – Physiological and Molecular Plant Pathology

Structure and Diversity of Soil Bacterial Communities in Offshore Islands – Lin – Scientific Reports

The effect of environment on the microbiome associated with the roots of a native woody plant under different climate types in China – Chen – Applied Microbiology and Biotechnology

Variation in rhizosphere priming and microbial growth and carbon use efficiency caused by wheat genotypes and temperatures – Yin – Soil Biology and Biochemistry

Using a soil bacterial species balance index to estimate potato crop productivity – Jeanne – PLoS One

Limited effect of planting transgenic rice on the soil microbiome studied by continuous 13CO2 labeling combined with high-throughput sequencing – Wang – Applied Microbiology and Biotechnology

Range-expansion effects on the belowground plant microbiome – Ramirez – Nature Ecology and Evolution

Water and extremophile microbiome

Environmental filtering determines family-level structure of sulfate-reducing microbial communities in subsurface marine sediments – Marshall – ISME

Built environment

Exploring the long-term effect of plastic on compost microbiome – Esan – PLoS One

An integrated microbiological and electrochemical approach to determine distributions of Fe metabolism in acid mine drainage-induced “iron mound” sediments – Leitholf – PLoS One

Probiotics/prebiotics

Strain-level diversity of commercial probiotic isolates of Bacillus, Lactobacillus, and Saccharomyces species illustrated by molecular identification and phenotypic profiling – Ansari – PLoS One

Review: Importance of probiotics in the prevention and treatment of colorectal cancer – Eslami – Journal of Cellular Physiology

Techniques

Robust sampling and preservation of DNA for microbial community profiling in field experiments – Groenenboom – BMC Research Notes

January 31, 2019

Today’s digest covers articles describing sphingolipids in host-microbiome interaction, unique microbiome and metabolome of Indian population, selection and stabilization of soil microbiome and effect of probiotics on early sepsis in patients and immune response in childrenEnjoy reading!

General microbiome

Metabolic Modeling of Human Gut Microbiota on a Genome Scale: An Overview – Partho Sen – Metabolites

Altered composition and function of intestinal microbiota in autism spectrum disorders: a systematic review – Feitong Liu – Translational Psychiatry

Sphingolipids in host–microbial interactions – Stacey L. Heaver – Current Opinion in Microbiology

Pregnancy and early life

Mixed Viral-Bacterial Infections and Their Effects on Gut Microbiota and Clinical Illnesses in Children – Shilu Mathew – Scientific Reports

Pathways linking caesarean delivery to early health in a dual burden context: Immune development and the gut microbiome in infants and children from Galápagos, Ecuador – Amanda L. Thompson – American Journal of Human Biology

Human gut microbiome

The vagino-cervical microbiome as a woman’s life history – Zhuye Jie – BioRxiv

Dynamics of Human Gut Microbiota and Short-Chain Fatty Acids in Response to Dietary Interventions with Three Fermentable Fibers – Nielson T. Baxter – mBio

The unique composition of Indian gut microbiome, gene catalogue and associated faecal metabolome deciphered using multi-omics approaches – D.B. Dhakan – Gigascience

Animal experiments

Oral neonatal antibiotic treatment perturbs gut microbiota and aggravates central nervous system autoimmunity in Dark Agouti rats – Suzana Stanisavljević – Scientific Reports

Intestinal epithelial N-acylphosphatidylethanolamine phospholipase D links dietary fat to metabolic adaptations in obesity and steatosis – Amandine Everard – Nature Communications

Mutual interplay between IL-17–producing γδT cells and microbiota orchestrates oral mucosal homeostasis – Anneke Wilharm – PNAS

Plant, root and soil microbiome

Selection, succession and stabilization of soil microbial consortia – Elias K. Zegeye – BioRxiv

Comparison of the bacterial and methanotrophic diversities between an Italian paddy field and its neighboring meadow – Mohammad Ghashghavi – BioRxiv

Quality of Irrigation Water Affects Soil Functionality and Bacterial Community Stability in Response to Heat Disturbance – Sammy Frenk – Applied and Environmental Microbiology

Water and extremophiles microbiome

Archaea dominate the microbial community in an ecosystem with low-to-moderate temperature and extreme acidity – Aleksei A. Korzhenkov – Microbiome

Antibiotic disturbance affects aquatic microbial community composition and foodweb interactions but not community resilience – Ester M. Eckert – Molecular Ecology

 Phages and viruses

Megaphages infect Prevotella and variants are widespread in gut microbiomes – Audra E. Devoto – Nature Microbiology

Probiotics / prebiotics

Dysbiosis in early sepsis can be modulated by a multispecies probiotic: a randomised controlled pilot trial – V. Stadlbauer – Beneficial Microbes

Lactobacillus plantarum IS-10506 supplementation increases faecal sIgA and immune response in children younger than two years – P.D. Kusumo – Beneficial Microbes

Supplementation with Lactobacillus kefiranofaciens ZW3 from Tibetan Kefir improves depression-like behavior in stressed mice by modulating the gut microbiota – Ye Sun – Food and Function

Non-microbiology picks

Identification of Enteroendocrine Regulators by Real-Time Single-Cell Differentiation Mapping – Helmuth Gehart – Cell